I'm sure you will be successful elsewhere, i know Japanese who failed to get their DTV in Japan but got it in SEA. As a Toyko resident myself I chose to get it elsewhere as it would be much quicker and less stress.
Japan especially Tokyo wants you to strongly demonstrate your need for a 5 year visa. Did you make use of their pre application service? Your 6 month visa gives you nearly 9 months stay in Thailand. Apply again nearby in SE Asia.
I know a couple of people who started MT in CM and moved to BKK with different schools, it is ok to do as you are continuing the activity you were awarded the DTV for.